Thermodynamics of alpha- and beta-structure formation in proteins

Abstract

An atomic protein model with a minimalistic potential is developed and then tested on an alpha-helix and a beta-hairpin, using exactly the same parameters for both peptides. We find that melting curves for these sequences to a good approximation can be described by a simple two-state model, with parameters that are in reasonable quantitative agreement with experimental data. Despite the apparent two-state character of the melting curves, the energy distributions are found to lack a clear bimodal shape, which is discussed in some detail. We also perform a Monte Carlo-based kinetic study and find, in accord with experimental data, that the alpha-helix forms faster than the beta-hairpin.

18 pages, 4 figures

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• Ab initio theory of helix-coil phase transition
• Two-state folding over a weak free-energy barrier
• Structural Properties of Small Semiconductor-Binding Synthetic Peptides
• What thermodynamic features characterize good and bad folders? Results from a simplified off-lattice protein model
• Folding thermodynamics of three beta-sheet peptides: A model study
• Efficient Microcanonical Histogram Analysis and Application to Peptide Aggregation